EHV-1 TES dynamics
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
TES dynamics
Those reads were counted only, where the 3-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.## Bootstrap (r = 0.6)... Done.## Bootstrap (r = 0.68)... Done.## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.38)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 4: 1 ORF17 1.0000000 1.0000000 1.0000000
## 5: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 6: 1 ORF30 1.0000000 1.0000000 1.0000000
## 7: 1 ORF31 1.0000000 1.0000000 1.0000000
## 8: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 9: 1 ORF63 1.0000000 1.0000000 1.0000000
## 10: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 11: 1 ORF65_1 1.0000000 1.0000000 1.0000000
## 12: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 15: 2 ORF2 0.9991266 0.9997380 0.9922209
## 16: 2 ORF3 0.9991266 0.9997380 0.9922209
## 17: 2 ORF8 0.9991266 0.9997380 0.9922209
## 18: 2 ORF9 0.9991266 0.9997380 0.9922209
## 19: 2 ORF12, ORF13, ORF14 0.9991266 0.9997380 0.9922209
## 20: 2 ORF18 0.9991266 0.9997380 0.9922209
## 21: 2 ORF22 0.9991266 0.9997380 0.9922209
## 22: 2 ORF23 0.9991266 0.9997380 0.9922209
## 23: 2 ORF27, ORF26, ORF25 0.9991266 0.9997380 0.9922209
## 24: 2 ORF28, ORF29 0.9991266 0.9997380 0.9922209
## 25: 2 ORF37, ORF36, ORF35, ORF35.5 0.9991266 0.9997380 0.9922209
## 26: 2 ORF36 0.9991266 0.9997380 0.9922209
## 27: 2 ORF37 0.9991266 0.9997380 0.9922209
## 28: 2 ORF38 0.9991266 0.9997380 0.9922209
## 29: 2 CTO 0.9991266 0.9997380 0.9922209
## 30: 2 ORF40 0.9991266 0.9997380 0.9922209
## 31: 2 ORF41, ORF42, OF43 0.9991266 0.9997380 0.9922209
## 32: 2 ORF44 0.9991266 0.9997380 0.9922209
## 33: 2 ORF48, ORF49, ORF50, ORF51 0.9991266 0.9997380 0.9922209
## 34: 2 ORF66_1 0.9991266 0.9997380 0.9922209
## 35: 3 ORF4 0.1542545 0.6250182 0.5135008
## 36: 3 ORF64_1 0.1542545 0.6250182 0.5135008
## 37: 3 ORF69, ORF70 0.1542545 0.6250182 0.5135008
## 38: 4 ORF18, ORF17, ORF16, ORF15 0.9868569 0.9962167 0.9396069
## 39: 4 ORF19 0.9868569 0.9962167 0.9396069
## 40: 4 ORF24 0.9868569 0.9962167 0.9396069
## 41: 4 ORF52 0.9868569 0.9962167 0.9396069
## 42: 4 ORF53, ORF54 0.9868569 0.9962167 0.9396069
## 43: 4 ORF57, ORF58 0.9868569 0.9962167 0.9396069
## 44: 4 ORF62, ORF61, ORF60,ORF59 0.9868569 0.9962167 0.9396069
## 45: 4 ORF71, ORF72, ORF73 0.9868569 0.9962167 0.9396069
## 46: 5 ORF39 0.3203290 0.6847526 0.6176900
## 47: 5 ORF45, ORF46 0.3203290 0.6847526 0.6176900
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 2: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 3: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 4: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 5: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 6: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 7: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 8: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 9: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 10: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 11: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 12: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 13: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 14: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 15: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 16: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 17: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 18: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 19: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 20: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 21: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 22: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 23: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 24: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 25: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 26: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 27: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 28: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 29: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 30: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 31: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 32: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 33: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 34: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 35: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 36: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 37: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 38: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 39: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 40: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 41: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 42: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 43: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 44: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 45: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 46: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.4001334
## 47: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.4001334
## se.si se.au se.bp v c pchi
## [1] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43" "ORF24"## [1] 4## [1] "ORF4" "ORF64_1" "ORF69, ORF70" "ORF39" "ORF45, ORF46"## [1] 5Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 4: 1 ORF17 1.0000000 1.0000000 1.0000000
## 5: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 6: 1 ORF30 1.0000000 1.0000000 1.0000000
## 7: 1 ORF31 1.0000000 1.0000000 1.0000000
## 8: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 9: 1 ORF63 1.0000000 1.0000000 1.0000000
## 10: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 11: 1 ORF65_1 1.0000000 1.0000000 1.0000000
## 12: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 15: 2 ORF2 0.9991266 0.9997380 0.9922209
## 16: 2 ORF3 0.9991266 0.9997380 0.9922209
## 17: 2 ORF8 0.9991266 0.9997380 0.9922209
## 18: 2 ORF9 0.9991266 0.9997380 0.9922209
## 19: 2 ORF12, ORF13, ORF14 0.9991266 0.9997380 0.9922209
## 20: 2 ORF18 0.9991266 0.9997380 0.9922209
## 21: 2 ORF22 0.9991266 0.9997380 0.9922209
## 22: 2 ORF23 0.9991266 0.9997380 0.9922209
## 23: 2 ORF27, ORF26, ORF25 0.9991266 0.9997380 0.9922209
## 24: 2 ORF28, ORF29 0.9991266 0.9997380 0.9922209
## 25: 2 ORF37, ORF36, ORF35, ORF35.5 0.9991266 0.9997380 0.9922209
## 26: 2 ORF36 0.9991266 0.9997380 0.9922209
## 27: 2 ORF37 0.9991266 0.9997380 0.9922209
## 28: 2 ORF38 0.9991266 0.9997380 0.9922209
## 29: 2 CTO 0.9991266 0.9997380 0.9922209
## 30: 2 ORF40 0.9991266 0.9997380 0.9922209
## 31: 2 ORF41, ORF42, OF43 0.9991266 0.9997380 0.9922209
## 32: 2 ORF44 0.9991266 0.9997380 0.9922209
## 33: 2 ORF48, ORF49, ORF50, ORF51 0.9991266 0.9997380 0.9922209
## 34: 2 ORF66_1 0.9991266 0.9997380 0.9922209
## 35: 3 ORF4 0.1542545 0.6250182 0.5135008
## 36: 3 ORF69, ORF70 0.1542545 0.6250182 0.5135008
## 37: 4 ORF18, ORF17, ORF16, ORF15 0.9868569 0.9962167 0.9396069
## 38: 4 ORF19 0.9868569 0.9962167 0.9396069
## 39: 4 ORF24 0.9868569 0.9962167 0.9396069
## 40: 4 ORF52 0.9868569 0.9962167 0.9396069
## 41: 4 ORF53, ORF54 0.9868569 0.9962167 0.9396069
## 42: 4 ORF57, ORF58 0.9868569 0.9962167 0.9396069
## 43: 4 ORF62, ORF61, ORF60,ORF59 0.9868569 0.9962167 0.9396069
## 44: 4 ORF71, ORF72, ORF73 0.9868569 0.9962167 0.9396069
## 45: 5 ORF39 0.3203290 0.6847526 0.6176900
## 46: 5 ORF45, ORF46 0.3203290 0.6847526 0.6176900
## 47: 6 ORF64_1 0.8511989 0.9443068 0.8291754
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 2: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 3: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 4: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 5: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 6: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 7: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 8: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 9: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 10: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 11: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 12: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 13: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 14: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 15: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 16: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 17: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 18: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 19: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 20: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 21: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 22: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 23: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 24: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 25: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 26: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 27: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 28: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 29: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 30: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 31: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 32: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 33: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 34: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 35: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 36: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 37: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 38: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 39: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 40: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 41: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 42: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 43: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 44: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 45: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.4001334
## 46: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.4001334
## 47: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.6157236
## se.si se.au se.bp v c pchi
## [1] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43" "ORF24"## [1] 4## [1] "ORF4" "ORF69, ORF70" "ORF39" "ORF45, ORF46" "ORF64_1"## [1] 5Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 4: 1 ORF17 1.0000000 1.0000000 1.0000000
## 5: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 6: 1 ORF30 1.0000000 1.0000000 1.0000000
## 7: 1 ORF31 1.0000000 1.0000000 1.0000000
## 8: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 9: 1 ORF63 1.0000000 1.0000000 1.0000000
## 10: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 11: 1 ORF65_1 1.0000000 1.0000000 1.0000000
## 12: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 15: 2 ORF2 0.9991266 0.9997380 0.9922209
## 16: 2 ORF3 0.9991266 0.9997380 0.9922209
## 17: 2 ORF8 0.9991266 0.9997380 0.9922209
## 18: 2 ORF9 0.9991266 0.9997380 0.9922209
## 19: 2 ORF12, ORF13, ORF14 0.9991266 0.9997380 0.9922209
## 20: 2 ORF18 0.9991266 0.9997380 0.9922209
## 21: 2 ORF22 0.9991266 0.9997380 0.9922209
## 22: 2 ORF23 0.9991266 0.9997380 0.9922209
## 23: 2 ORF27, ORF26, ORF25 0.9991266 0.9997380 0.9922209
## 24: 2 ORF28, ORF29 0.9991266 0.9997380 0.9922209
## 25: 2 ORF37, ORF36, ORF35, ORF35.5 0.9991266 0.9997380 0.9922209
## 26: 2 ORF36 0.9991266 0.9997380 0.9922209
## 27: 2 ORF37 0.9991266 0.9997380 0.9922209
## 28: 2 ORF38 0.9991266 0.9997380 0.9922209
## 29: 2 CTO 0.9991266 0.9997380 0.9922209
## 30: 2 ORF40 0.9991266 0.9997380 0.9922209
## 31: 2 ORF41, ORF42, OF43 0.9991266 0.9997380 0.9922209
## 32: 2 ORF44 0.9991266 0.9997380 0.9922209
## 33: 2 ORF48, ORF49, ORF50, ORF51 0.9991266 0.9997380 0.9922209
## 34: 2 ORF66_1 0.9991266 0.9997380 0.9922209
## 35: 3 ORF4 0.1542545 0.6250182 0.5135008
## 36: 3 ORF69, ORF70 0.1542545 0.6250182 0.5135008
## 37: 4 ORF18, ORF17, ORF16, ORF15 0.9868569 0.9962167 0.9396069
## 38: 4 ORF19 0.9868569 0.9962167 0.9396069
## 39: 4 ORF52 0.9868569 0.9962167 0.9396069
## 40: 4 ORF53, ORF54 0.9868569 0.9962167 0.9396069
## 41: 4 ORF57, ORF58 0.9868569 0.9962167 0.9396069
## 42: 4 ORF62, ORF61, ORF60,ORF59 0.9868569 0.9962167 0.9396069
## 43: 4 ORF71, ORF72, ORF73 0.9868569 0.9962167 0.9396069
## 44: 5 ORF24 0.3203290 0.6847526 0.6176900
## 45: 6 ORF39 0.8511989 0.9443068 0.8291754
## 46: 6 ORF45, ORF46 0.8511989 0.9443068 0.8291754
## 47: 7 ORF64_1 0.9974425 0.9993234 0.9741571
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 2: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 3: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 4: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 5: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 6: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 7: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 8: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 9: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 10: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 11: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 12: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 13: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 14: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 15: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 16: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 17: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 18: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 19: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 20: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 21: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 22: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 23: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 24: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 25: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 26: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 27: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 28: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 29: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 30: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 31: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 32: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 33: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 34: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 35: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 36: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 37: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 38: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 39: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 40: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 41: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 42: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 43: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 44: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.4001334
## 45: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.6157236
## 46: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.6157236
## 47: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.9302770
## se.si se.au se.bp v c pchi
## [1] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"## [1] 3## [1] "ORF4" "ORF69, ORF70" "ORF24" "ORF39" "ORF45, ORF46"## [1] 5Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF17 1.0000000 1.0000000 1.0000000
## 3: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 4: 1 ORF31 1.0000000 1.0000000 1.0000000
## 5: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 6: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 7: 2 ORF2 0.9991266 0.9997380 0.9922209
## 8: 2 ORF8 0.9991266 0.9997380 0.9922209
## 9: 2 ORF12, ORF13, ORF14 0.9991266 0.9997380 0.9922209
## 10: 2 ORF22 0.9991266 0.9997380 0.9922209
## 11: 2 ORF23 0.9991266 0.9997380 0.9922209
## 12: 2 ORF27, ORF26, ORF25 0.9991266 0.9997380 0.9922209
## 13: 2 ORF37, ORF36, ORF35, ORF35.5 0.9991266 0.9997380 0.9922209
## 14: 2 ORF36 0.9991266 0.9997380 0.9922209
## 15: 2 CTO 0.9991266 0.9997380 0.9922209
## 16: 2 ORF40 0.9991266 0.9997380 0.9922209
## 17: 2 ORF41, ORF42, OF43 0.9991266 0.9997380 0.9922209
## 18: 2 ORF44 0.9991266 0.9997380 0.9922209
## 19: 3 ORF3 0.1542545 0.6250182 0.5135008
## 20: 3 ORF9 0.1542545 0.6250182 0.5135008
## 21: 3 ORF18 0.1542545 0.6250182 0.5135008
## 22: 3 ORF28, ORF29 0.1542545 0.6250182 0.5135008
## 23: 3 ORF37 0.1542545 0.6250182 0.5135008
## 24: 3 ORF38 0.1542545 0.6250182 0.5135008
## 25: 3 ORF48, ORF49, ORF50, ORF51 0.1542545 0.6250182 0.5135008
## 26: 3 ORF66_1 0.1542545 0.6250182 0.5135008
## 27: 4 ORF4 0.9868569 0.9962167 0.9396069
## 28: 4 ORF69, ORF70 0.9868569 0.9962167 0.9396069
## 29: 5 ORF7, ORF6, ORF5 0.3203290 0.6847526 0.6176900
## 30: 5 ORF30 0.3203290 0.6847526 0.6176900
## 31: 5 ORF63 0.3203290 0.6847526 0.6176900
## 32: 5 ORF65_1 0.3203290 0.6847526 0.6176900
## 33: 6 ORF10, ORF11 0.8511989 0.9443068 0.8291754
## 34: 6 ORF32, ORF33, ORF34 0.8511989 0.9443068 0.8291754
## 35: 6 NOIR_1 0.8511989 0.9443068 0.8291754
## 36: 6 NOIR_2 0.8511989 0.9443068 0.8291754
## 37: 7 ORF18, ORF17, ORF16, ORF15 0.9974425 0.9993234 0.9741571
## 38: 7 ORF19 0.9974425 0.9993234 0.9741571
## 39: 7 ORF52 0.9974425 0.9993234 0.9741571
## 40: 7 ORF53, ORF54 0.9974425 0.9993234 0.9741571
## 41: 7 ORF57, ORF58 0.9974425 0.9993234 0.9741571
## 42: 7 ORF62, ORF61, ORF60,ORF59 0.9974425 0.9993234 0.9741571
## 43: 7 ORF71, ORF72, ORF73 0.9974425 0.9993234 0.9741571
## 44: 8 ORF24 0.6703701 0.9283232 0.4608557
## 45: 9 ORF39 0.9975747 0.9994822 0.9546715
## 46: 9 ORF45, ORF46 0.9975747 0.9994822 0.9546715
## 47: 10 ORF64_1 0.2469763 0.7002385 0.5033637
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 2: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 3: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 4: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 5: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 6: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.0000000
## 7: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 8: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 9: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 10: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 11: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 12: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 13: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 14: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 15: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 16: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 17: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 18: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.6661652
## 19: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 20: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 21: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 22: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 23: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 24: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 25: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 26: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.2099825
## 27: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 28: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.8704015
## 29: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.4001334
## 30: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.4001334
## 31: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.4001334
## 32: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.4001334
## 33: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.6157236
## 34: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.6157236
## 35: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.6157236
## 36: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.6157236
## 37: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.9302770
## 38: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.9302770
## 39: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.9302770
## 40: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.9302770
## 41: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.9302770
## 42: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.9302770
## 43: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.9302770
## 44: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.2673777
## 45: 0.0008791163 0.0002241674 0.002493679 -2.4863140 0.79437129 0.6616117
## 46: 0.0008791163 0.0002241674 0.002493679 -2.4863140 0.79437129 0.6616117
## 47: 0.0409402876 0.0266612997 0.005274842 -0.2667591 0.25832756 0.9661312
## se.si se.au se.bp v c pchi
## character(0)## [1] 0## [1] "ORF3" "ORF9"
## [3] "ORF18" "ORF28, ORF29"
## [5] "ORF37" "ORF38"
## [7] "ORF48, ORF49, ORF50, ORF51" "ORF66_1"
## [9] "ORF7, ORF6, ORF5" "ORF30"
## [11] "ORF63" "ORF65_1"
## [13] "ORF10, ORF11" "ORF32, ORF33, ORF34"
## [15] "NOIR_1" "NOIR_2"
## [17] "ORF24" "ORF64_1"## [1] 18Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF17 1.0000000 1.0000000 1.0000000
## 3: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 4: 1 ORF31 1.0000000 1.0000000 1.0000000
## 5: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 6: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 7: 2 ORF2 0.9991266 0.9997380 0.9922209
## 8: 2 ORF40 0.9991266 0.9997380 0.9922209
## 9: 3 ORF3 0.1542545 0.6250182 0.5135008
## 10: 3 ORF9 0.1542545 0.6250182 0.5135008
## 11: 3 ORF18 0.1542545 0.6250182 0.5135008
## 12: 3 ORF28, ORF29 0.1542545 0.6250182 0.5135008
## 13: 3 ORF37 0.1542545 0.6250182 0.5135008
## 14: 3 ORF38 0.1542545 0.6250182 0.5135008
## 15: 3 ORF48, ORF49, ORF50, ORF51 0.1542545 0.6250182 0.5135008
## 16: 3 ORF66_1 0.1542545 0.6250182 0.5135008
## 17: 4 ORF4 0.9868569 0.9962167 0.9396069
## 18: 5 ORF7, ORF6, ORF5 0.3203290 0.6847526 0.6176900
## 19: 5 ORF30 0.3203290 0.6847526 0.6176900
## 20: 5 ORF63 0.3203290 0.6847526 0.6176900
## 21: 5 ORF65_1 0.3203290 0.6847526 0.6176900
## 22: 6 ORF8 0.8511989 0.9443068 0.8291754
## 23: 6 ORF12, ORF13, ORF14 0.8511989 0.9443068 0.8291754
## 24: 6 ORF22 0.8511989 0.9443068 0.8291754
## 25: 6 ORF23 0.8511989 0.9443068 0.8291754
## 26: 6 ORF27, ORF26, ORF25 0.8511989 0.9443068 0.8291754
## 27: 6 ORF37, ORF36, ORF35, ORF35.5 0.8511989 0.9443068 0.8291754
## 28: 6 ORF36 0.8511989 0.9443068 0.8291754
## 29: 6 CTO 0.8511989 0.9443068 0.8291754
## 30: 6 ORF41, ORF42, OF43 0.8511989 0.9443068 0.8291754
## 31: 6 ORF44 0.8511989 0.9443068 0.8291754
## 32: 7 ORF10, ORF11 0.9974425 0.9993234 0.9741571
## 33: 7 ORF32, ORF33, ORF34 0.9974425 0.9993234 0.9741571
## 34: 7 NOIR_1 0.9974425 0.9993234 0.9741571
## 35: 7 NOIR_2 0.9974425 0.9993234 0.9741571
## 36: 8 ORF18, ORF17, ORF16, ORF15 0.6703701 0.9283232 0.4608557
## 37: 8 ORF19 0.6703701 0.9283232 0.4608557
## 38: 8 ORF52 0.6703701 0.9283232 0.4608557
## 39: 8 ORF53, ORF54 0.6703701 0.9283232 0.4608557
## 40: 8 ORF57, ORF58 0.6703701 0.9283232 0.4608557
## 41: 8 ORF62, ORF61, ORF60,ORF59 0.6703701 0.9283232 0.4608557
## 42: 8 ORF71, ORF72, ORF73 0.6703701 0.9283232 0.4608557
## 43: 9 ORF24 0.9975747 0.9994822 0.9546715
## 44: 10 ORF39 0.2469763 0.7002385 0.5033637
## 45: 10 ORF45, ORF46 0.2469763 0.7002385 0.5033637
## 46: 11 ORF64_1 0.3312188 0.7072472 0.5917159
## 47: 12 ORF69, ORF70 0.8105730 0.9523923 0.6284884
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 2: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 3: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 4: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 5: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 6: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 7: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.66616516
## 8: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.66616516
## 9: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 10: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 11: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 12: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 13: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 14: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 15: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 16: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 17: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.87040148
## 18: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.40013340
## 19: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.40013340
## 20: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.40013340
## 21: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.40013340
## 22: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 23: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 24: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 25: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 26: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 27: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 28: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 29: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 30: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 31: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 32: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.93027701
## 33: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.93027701
## 34: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.93027701
## 35: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.93027701
## 36: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 37: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 38: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 39: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 40: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 41: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 42: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 43: 0.0008791163 0.0002241674 0.002493679 -2.4863140 0.79437129 0.66161174
## 44: 0.0409402876 0.0266612997 0.005274842 -0.2667591 0.25832756 0.96613122
## 45: 0.0409402876 0.0266612997 0.005274842 -0.2667591 0.25832756 0.96613122
## 46: 0.0389819668 0.0264953779 0.005197512 -0.3886608 0.15669962 0.02980103
## 47: 0.0222722968 0.0077972867 0.005179177 -0.9981791 0.67032662 0.86210841
## se.si se.au se.bp v c pchi
## [1] "ORF28, ORF29" "ORF66_1"## [1] 2## [1] "ORF3" "ORF9"
## [3] "ORF18" "ORF28, ORF29"
## [5] "ORF37" "ORF38"
## [7] "ORF48, ORF49, ORF50, ORF51" "ORF66_1"
## [9] "ORF7, ORF6, ORF5" "ORF30"
## [11] "ORF63" "ORF65_1"
## [13] "ORF8" "ORF12, ORF13, ORF14"
## [15] "ORF22" "ORF23"
## [17] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [19] "ORF36" "CTO"
## [21] "ORF41, ORF42, OF43" "ORF44"
## [23] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [25] "ORF52" "ORF53, ORF54"
## [27] "ORF57, ORF58" "ORF62, ORF61, ORF60,ORF59"
## [29] "ORF71, ORF72, ORF73" "ORF39"
## [31] "ORF45, ORF46" "ORF64_1"## [1] 32Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF17 1.0000000 1.0000000 1.0000000
## 3: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 4: 1 ORF31 1.0000000 1.0000000 1.0000000
## 5: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 6: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 7: 2 ORF2 0.9991266 0.9997380 0.9922209
## 8: 2 ORF40 0.9991266 0.9997380 0.9922209
## 9: 3 ORF3 0.1542545 0.6250182 0.5135008
## 10: 3 ORF9 0.1542545 0.6250182 0.5135008
## 11: 3 ORF18 0.1542545 0.6250182 0.5135008
## 12: 3 ORF28, ORF29 0.1542545 0.6250182 0.5135008
## 13: 3 ORF37 0.1542545 0.6250182 0.5135008
## 14: 3 ORF38 0.1542545 0.6250182 0.5135008
## 15: 3 ORF48, ORF49, ORF50, ORF51 0.1542545 0.6250182 0.5135008
## 16: 3 ORF66_1 0.1542545 0.6250182 0.5135008
## 17: 4 ORF4 0.9868569 0.9962167 0.9396069
## 18: 5 ORF7, ORF6, ORF5 0.3203290 0.6847526 0.6176900
## 19: 5 ORF30 0.3203290 0.6847526 0.6176900
## 20: 5 ORF63 0.3203290 0.6847526 0.6176900
## 21: 5 ORF65_1 0.3203290 0.6847526 0.6176900
## 22: 6 ORF8 0.8511989 0.9443068 0.8291754
## 23: 6 ORF12, ORF13, ORF14 0.8511989 0.9443068 0.8291754
## 24: 6 ORF22 0.8511989 0.9443068 0.8291754
## 25: 6 ORF23 0.8511989 0.9443068 0.8291754
## 26: 6 ORF27, ORF26, ORF25 0.8511989 0.9443068 0.8291754
## 27: 6 ORF37, ORF36, ORF35, ORF35.5 0.8511989 0.9443068 0.8291754
## 28: 6 ORF36 0.8511989 0.9443068 0.8291754
## 29: 6 CTO 0.8511989 0.9443068 0.8291754
## 30: 6 ORF41, ORF42, OF43 0.8511989 0.9443068 0.8291754
## 31: 6 ORF44 0.8511989 0.9443068 0.8291754
## 32: 7 ORF10, ORF11 0.9974425 0.9993234 0.9741571
## 33: 7 ORF32, ORF33, ORF34 0.9974425 0.9993234 0.9741571
## 34: 7 NOIR_1 0.9974425 0.9993234 0.9741571
## 35: 7 NOIR_2 0.9974425 0.9993234 0.9741571
## 36: 8 ORF18, ORF17, ORF16, ORF15 0.6703701 0.9283232 0.4608557
## 37: 8 ORF19 0.6703701 0.9283232 0.4608557
## 38: 8 ORF52 0.6703701 0.9283232 0.4608557
## 39: 8 ORF53, ORF54 0.6703701 0.9283232 0.4608557
## 40: 8 ORF57, ORF58 0.6703701 0.9283232 0.4608557
## 41: 8 ORF62, ORF61, ORF60,ORF59 0.6703701 0.9283232 0.4608557
## 42: 8 ORF71, ORF72, ORF73 0.6703701 0.9283232 0.4608557
## 43: 9 ORF24 0.9975747 0.9994822 0.9546715
## 44: 10 ORF39 0.2469763 0.7002385 0.5033637
## 45: 10 ORF45, ORF46 0.2469763 0.7002385 0.5033637
## 46: 11 ORF64_1 0.3312188 0.7072472 0.5917159
## 47: 12 ORF69, ORF70 0.8105730 0.9523923 0.6284884
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 2: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 3: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 4: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 5: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 6: 0.0000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.00000000
## 7: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.66616516
## 8: 0.0006288161 0.0002153324 0.001135391 -2.9436585 0.52454192 0.66616516
## 9: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 10: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 11: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 12: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 13: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 14: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 15: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 16: 0.0386716801 0.0290122871 0.005271875 -0.1762677 0.14241966 0.20998250
## 17: 0.0036853369 0.0012812649 0.002785563 -2.1111533 0.55967111 0.87040148
## 18: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.40013340
## 19: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.40013340
## 20: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.40013340
## 21: 0.0384289690 0.0275376190 0.005139443 -0.3902250 0.09080546 0.40013340
## 22: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 23: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 24: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 25: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 26: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 27: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 28: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 29: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 30: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 31: 0.0203200015 0.0098533942 0.004101773 -1.2714523 0.32054051 0.61572364
## 32: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.93027701
## 33: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.93027701
## 34: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.93027701
## 35: 0.0010965484 0.0003405664 0.001931852 -2.5750955 0.62935458 0.93027701
## 36: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 37: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 38: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 39: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 40: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 41: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 42: 0.0330352546 0.0107602365 0.005282016 -0.6825690 0.78084714 0.26737771
## 43: 0.0008791163 0.0002241674 0.002493679 -2.4863140 0.79437129 0.66161174
## 44: 0.0409402876 0.0266612997 0.005274842 -0.2667591 0.25832756 0.96613122
## 45: 0.0409402876 0.0266612997 0.005274842 -0.2667591 0.25832756 0.96613122
## 46: 0.0389819668 0.0264953779 0.005197512 -0.3886608 0.15669962 0.02980103
## 47: 0.0222722968 0.0077972867 0.005179177 -0.9981791 0.67032662 0.86210841
## se.si se.au se.bp v c pchi
## [1] "ORF28, ORF29" "ORF66_1"## [1] 2## [1] "ORF3" "ORF9"
## [3] "ORF18" "ORF28, ORF29"
## [5] "ORF37" "ORF38"
## [7] "ORF48, ORF49, ORF50, ORF51" "ORF66_1"
## [9] "ORF7, ORF6, ORF5" "ORF30"
## [11] "ORF63" "ORF65_1"
## [13] "ORF8" "ORF12, ORF13, ORF14"
## [15] "ORF22" "ORF23"
## [17] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [19] "ORF36" "CTO"
## [21] "ORF41, ORF42, OF43" "ORF44"
## [23] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [25] "ORF52" "ORF53, ORF54"
## [27] "ORF57, ORF58" "ORF62, ORF61, ORF60,ORF59"
## [29] "ORF71, ORF72, ORF73" "ORF39"
## [31] "ORF45, ORF46" "ORF64_1"## [1] 32Remove genes from clusters ?
## [1] "ORF3" "ORF9"
## [3] "ORF18" "ORF28, ORF29"
## [5] "ORF37" "ORF38"
## [7] "ORF48, ORF49, ORF50, ORF51" "ORF66_1"
## [9] "ORF7, ORF6, ORF5" "ORF30"
## [11] "ORF63" "ORF65_1"
## [13] "ORF8" "ORF12, ORF13, ORF14"
## [15] "ORF22" "ORF23"
## [17] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [19] "ORF36" "CTO"
## [21] "ORF41, ORF42, OF43" "ORF44"
## [23] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [25] "ORF52" "ORF53, ORF54"
## [27] "ORF57, ORF58" "ORF62, ORF61, ORF60,ORF59"
## [29] "ORF71, ORF72, ORF73" "ORF39"
## [31] "ORF45, ORF46" "ORF64_1"## [1] 32## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 6 10
## 2: 3 8
## 3: 8 7
## 4: 1 6
## 5: 5 4
## 6: 7 4
## 7: 2 2
## 8: 10 2
## 9: 4 1
## 10: 9 1
## 11: 11 1
## 12: 12 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
